Biomedical subjects

S Succi

Publications and source records attributed to S Succi.

At least 19 recordsLinked to original sources

PubMed2006

Surface roughness-hydrophobicity coupling in microchannel and nanochannel flows.

An approach based on a lattice version of the Boltzmann kinetic equation for describing multiphase flows in nano- and microcorrugated devices is proposed. We specialize it to describe the wetting-dewetting transition of fluids in the presence of nanoscopic grooves etched on the boundaries. This approach permits us to retain the essential supramolecular details of fluid-solid interactions without surrendering--actually boosting--the computational efficiency of continuum methods. The method is used to analyze the importance of conspiring effects between hydrophobicity and roughness on the global mass flow rate of the microchannel. In particular we show that smart surfaces can be tailored to yield very different mass throughput by changing the bulk pressure. The mesoscopic method is also validated quantitatively against the molecular dynamics results of [Cottin-Bizonne, Nat. Mater. 2, 237 (2003)].

Journal Article↗

PubMed2006

Molecular dynamics simulation of ratchet motion in an asymmetric nanochannel.

The persistence of ratchet effects, i.e., nonzero mass flux under a zero-mean time-dependent drive, when many-body interactions are present, is studied via molecular dynamics (MD) simulations of a simple liquid flowing in an asymmetric nanopore. The results show that (i) ratchet effects persist under many-body density correlations induced by the forcing; (ii) two distinct linear responses (flux proportional to the drive amplitude) appear under strong loads. One regime has the same conductivity of linear response theory up to a forcing of about 10 kT, while the second displays a smaller conductivity, the difference in responses is due to geometric effects alone. (iii) Langevin simulations based on a naive mapping of the many-body equilibrium bulk diffusivity, D, onto the damping rate, gamma are also found to yield two distinct linear responses. However, in both regimes, the flux is significantly smaller than the one of MD simulations.

Computer Simulation↗

PubMed2006

Mesoscopic modeling of a two-phase flow in the presence of boundaries: The contact angle.

We present a mesoscopic model, based on the Boltzmann equation, for the interaction between a solid wall and a nonideal fluid. We present an analytic derivation of the contact angle in terms of the surface tension between the liquid-gas, the liquid-solid, and the gas-solid phases. We study the dependency of the contact angle on the two free parameters of the model, which determine the interaction between the fluid and the boundaries, i.e. the equivalent of the wall density and of the wall-fluid potential in molecular dynamics studies. We compare the analytical results obtained in the hydrodynamical limit for the density profile and for the surface tension expression with the numerical simulations. We compare also our two-phase approach with some exact results obtained by E. Lauga and H. Stone [J. Fluid. Mech. 489, 55 (2003)] and J. Philip [Z. Angew. Math. Phys. 23, 960 (1972)] for a pure hydrodynamical incompressible fluid based on Navier-Stokes equations with boundary conditions made up of alternating slip and no-slip strips. Finally, we show how to overcome some theoretical limitations connected with the discretized Boltzmann scheme proposed by X. Shan and H. Chen [Phys. Rev. E 49, 2941 (1994)] and we discuss the equivalence between the surface tension defined in terms of the mechanical equilibrium and in terms of the Maxwell construction.

Journal Article↗

PubMed2006

Lattice Boltzmann scheme for fluids with dynamic heterogeneities.

We introduce and discuss a three-dimensional mesoscopic lattice Boltzmann model for the numerical simulation of strongly-interacting fluids with dynamic inhomogeneities. The model is based on an extension of the standard lattice Boltzmann dynamics in which streaming between neighboring lattice sites is constrained by the value of the nonlocal density of the surrounding fluid. The resulting dynamics exhibits typical features of dynamically heterogeneous fluids, such as long-time relaxation, non-Gaussian density distributions and dynamic heterogeneities. Due to its intrinsically parallel dynamics and absence of statistical noise, the method is expected to compute significantly faster than molecular dynamics, Monte Carlo, and lattice glass models.

Journal Article↗

PubMed2005

Phase-field lattice kinetic scheme for the numerical simulation of dendritic growth.

A phase-field lattice kinetic model is presented for the numerical simulation of the dendritic growth of a pure crystal in the presence of thermal transport. A finite-difference scheme for the phase field is combined with an explicit lattice kinetic scheme for the temperature field. The resulting scheme is advanced in time with an adaptive time-marching procedure which permits us to achieve long simulation times with larger time steps than explicit finite-difference and previous kinetic methods. The method is demonstrated for the case of dendritic growth of a single crystal over a wide range of Stefan and capillarity numbers.

Journal Article↗

PubMed2005

Lattice mesoscopic model of dynamically heterogeneous fluids.

We introduce a mesoscopic three-dimensional lattice Boltzmann model which attempts to mimic the physical features associated with cage effects in dynamically heterogeneous fluids. To this purpose, we extend the standard lattice Boltzmann dynamics with self-consistent constraints based on the nonlocal density of the surrounding fluid. The resulting dynamics exhibits typical features of dynamic heterogeneous fluids, such as non-Gaussian density distributions and long-time relaxation. Because of its intrinsically parallel dynamics, and absence of statistical noise, the method is expected to compute significantly faster than molecular dynamics, Monte Carlo, and lattice glass models.

Journal Article↗

PubMed2005

Energy dissipation measures in three-dimensional disordered porous media.

The onset of nonlinear flow was analyzed in three-dimensional random, porous granular systems with 60% porosity using a lattice-Boltzmann model. Quantitative analysis was based on participation numbers built on local kinetic energies and energy dissipation rates computed via nonequilibrium kinetic (viscous stress) tensors. In contrast to the kinetic energy participation number, which characterizes the onset of nonlinearity in terms of a transition from a locally concentrated to a dispersed distribution of kinetic energy densities, the nonequilibrium kinetic tensor participation number characterizes the onset of nonlinearity in terms of a transition from a dispersed to a locally concentrated distribution of energy dissipation densities as the flow rate increases. The transition characterized by the nonequilibrium kinetic tensor participation number occurred over a nearly equal or a narrower range of Reynolds numbers when compared to the transition characterized by the kinetic energy participation number.

Journal Article↗

PubMed2004

Lattice Boltzmann schemes without coordinates.

We discuss recent developments extending the scope of the lattice Boltzmann method to unstructured (coordinateless) grids with arbitrary connectivity. Besides their intrinsic interest as examples of discrete kinetic systems living in irregular phase-space, the above extensions bear a direct relevance as computational tools for multi-scale applications.

Journal Article↗

PubMed2003

Lattice Boltzmann method on unstructured grids: further developments.

We discuss further developments of the finite-volume lattice Boltzmann formulation on unstructured grids. It is shown that the method tolerates significant grid distortions without showing any appreciable numerical viscosity effects at second order in the mesh size. A theoretical argument of plausibility for such a property is presented. In addition, a set of boundary conditions which permit to handle flows with open boundaries is also introduced and numerically demonstrated for the case of channel flows and driven cavity flows.

Journal Article↗

PubMed2002

Intracellular signal propagation in a two-dimensional autocatalytic reaction model.

We study a simple reaction scheme in a two-dimensional lattice of particles or molecules with a refractory state. We analyze the dynamics of the propagating front as a function of physical-chemical properties of the host medium. The anisotropy of the medium significantly affects the smoothness of the wave front. Similarly, if particles or molecules may diffuse slowly to neighboring sites, then the front wave is more likely to be irregular. Both situations affect the ability of the whole system to relax to the original state, which is a required feature in the biological cells. Attempts to map this simple reaction scheme to reactions involved in the intracellular pathways suggest that, in some cases, signal transduction might take both connotation of a random walk and a propagating wave, depending on the local density of the medium. In particular, a sufficient condition for the appearance of waves in high-density regions of the media, is the existence of at least one autocatalytic reaction in the chain of reactions characterizing the pathway.

Biophysical Phenomena↗

PubMed2001

Lattice Boltzmann model for anisotropic liquid-solid phase transition.

We develop a simple reaction model for the liquid-solid phase transition in the context of the lattice Boltzmann method with enhanced collisions. Calculations for a two-dimensional test problem of Ga melting and for a two-dimensional anisotropic growth of dendrites are presented and commented on.

Journal Article↗

PubMed2000

Large-scale cellular automata simulations of the immune system response.

The sequential nature of the process allowing the immune system to learn how to withstand pathogen agents is explored by means of large-scale computer simulation of the Celada-Seiden immunological automaton. In accord with our previous results, it is found that the learning process proceeds via a sequential cascade in affinity space.

B-Lymphocytes↗

PubMed2000

Numerical solution of the gross-pitaevskii equation using an explicit finite-difference scheme: An application to trapped bose-einstein condensates

We present the application of a fast, explicit time-marching scheme for the solution of the Gross-Pitaevskii equation in cylindrical geometry. The scheme is validated on simple analytical tests and demonstrated for two situations of physical interest in experiments on the Bose-Einstein condensation (BEC) of trapped alkali-metal vapors. It is tested by reproducing known results on the free expansion of a BEC after removing a cylindrical trap, and it is then used to address the formation of matter-wave pulses that result from gravity-induced transport of a condensate in an optical potential.

Journal Article↗

PubMed2000

Ground state of trapped interacting bose-einstein condensates by an explicit imaginary-time algorithm

We show that an explicit time-marching method previously developed for the numerical study of the dynamics of Bose-Einstein condensates can be profitably adapted to the numerical determination of their ground state. After reduction to a one-dimensional model, we first reproduce and test known results on condensates in harmonic traps and then determine the ground state of a condensate in a harmonically bound optical lattice in the range of parameters which are relevant to existing experiments.

Journal Article↗

PubMed1996